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< h1 id = "manipulated-sequences" > Manipulated sequences</ h1 >
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< li > We consider sequences only as compact form of a set of overlaping kmers</ li >
< li > The largest kmers we considere are 31-mer</ li >
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< p > We only consider odd k</ p >
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< p > all sequences match /^[acgtACGT]+/</ p >
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< li > maximum length 256 nucleotides</ li >
< li > minimum length k</ li >
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